This information has been taken from my reading of Cryptum and Primordium by Greg Bear and from Halo Nation. All errors are my own. Please feel free to make any corrections in the comments. I do not have any information about Halo 4 that is not in the public domain (with the exception of the leak copies of Halo 4 which I have not torrented or viewed) but this article may contain spoilers.
An Ancient Evil Awakens: This is the tagline for Halo 4. But what is that evil? Where does it come from and what has it been doing all this time?
One hundred thousand years ago, the Forerunners activated the Halo arrays, wiping out all intelligent life in the galaxy in order to deny food to the Flood. Approximately 10,000 years prior to this, the Forerunners defeat the humans in the Forerunner-Human war. However, the humans were winning this war until they were forced move significant resources to combat another threat. This other threat turns out to be the Flood. The humans defeat and find a cure against the Flood, but they are too weak to hold back the Forerunners.The Forerunners fail to gain the secret of the Flood cure from the humans, who hold it from them. After the war, the Forerunners discover a stasis capsule on Charum Hakkor containing the last of the Precursors, the race they defeated to become the leading race in the galaxy.
In preparing for conflict with the Flood, two competing solutions are offered. The Master Builder proposes the construction of a number of Halo arrays which will wipe out the Flood by killing all intelligent life in the galaxy, thereby denying it food. The Didact, the Forerunner military leader who waged the successful campaign against the humans, considers this plan a sin beyond measure against the Mantle, and proposes the construction of Shield Worlds (a shield world was seen in Halo Wars) around the galaxy to monitor and combat Flood outbreaks. When the Council chooses the Builder plan, the Didact is stripped of his power and goes into exile.
The Halo rings are built and one is successfully tested on Charum Hakkor. The Precursor is transferred to the Halo and interrogated. Mendicant Bias, the AI in charge of the interrogation, is convinced by the Precursor, who is a Gravemind, to defect to his cause. Mendicant Bias purposefully becomes rampant and assaults the Forerunner home system with five of the Halo arrays. The battle continues as the Mendicant Bias attempts to destroy the Forerunners and seize the Ark as they accelerate the completion of the arrays. The conflict is resolved with the arrays fired and the Flood defeated.
Halo 4 takes place on Requiem, a shield world. It seems obvious that the Precursor/Gravemind has survived and is imprisoned on Requiem and is able to escape, perhaps due to the actions of a Covenant splinter group or the humans on Infinity. We will have to wait until 6 November to find out.
Note: Any Halo 4 spoilers placed in the comments will be deleted.